Impacts of cytoplasmic inheritance on genetic evaluations

Simulation was used to examine the consequences of ignoring cytoplasmic effects on genetic evaluations. Effects on variance component estimation, accuracy of selection, genetic trend, and selection of bull-dams were considered. Comparisons were made for sire and animal models, several levels of cytoplasmic variance, and definition of cytoplasmic effects as either fixed or random. Ten replications with approximately 9000 cows and 20,000 records were simulated for each model and level of cytoplasmic variance. Derivative-free REML was used for estimation of variance components. Ignoring cytoplasmic effects caused overestimation of heritability with an animal model. Permanent environmental variance was underestimated with an animal model and overestimated with a sire model. Results were used for simulation of large (approximately 200,000 cow) data files for analysis of effects on accuracy of selection. Accuracy of selection increased when cytoplasmic effects were accounted for properly. Improvement of predicted breeding values was greater for cows than for sires and increased as cytoplasmic variance increased. Genetic trend also increased slightly, primarily as a function of increased accuracy of bull-dam selection. Little practical difference was detected when cytoplasmic effects were considered to be fixed rather than random.